I have two questions(contains spoilers)

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The evil Bakura from 5000 years ago used the Millennium Items to summon Zorc. When he did this, he was absorbed by Zorc and they became one. After Atem sealed away Zorc for the first time, Zorc put evil Bakura's soul in the Millennium Ring, and present day Bakura (the good one) was possessed by the evil Bakura whenever he wore it. Evil Bakura then went to the past with Atem, freed Zorc, and was reabsorbed by him once more after revealing that he was Zorc all along since they had merged the first time. It seems that when Zorc absorbed evil Bakura the first time, his personality completely took over evil Bakura's, so it was Zorc in control the whole time ever since, and he was just trying to free his main body from it's prison. To do this, he tried to rewrite the past.

It's confusing, but here's an easy break down:
Evil Bakura summons Zorc. Zorc absorbs evil Bakura, allowing him to take evil Bakura's form. Zorc is sealed away, but a portion of his soul remains free, which takes the form of evil Bakura, who dwells in the Millennium Ring. 5000 years later, evil Bakura possess good Bakura through the Millennium Ring. Evil Bakura's spirit leaves the Millennium Ring and goes to the past to before Zorc was summoned the first time. Evil Bakura summons Zorc and is absorbed once again the same way he was the first time. Zorc tries to change history by preventing Atem from sealing him away the way he did the first time. Atem seals Zorc away the same way he did the first time, but this time Zorc, but this time while still merged with Bakura, so he can no longer be freed.

As for Yugi and Atem (Yami's real name), yes, they do. After defeating Zorc once and for all, Atem and Yugi separate. It's revealed to everyone (including Kaiba) that Atem has been the one fighting all the duels the entire series, not Yugi since he almost always let Atem take over the duels, meaning he is the real king of games, not Yugi. Yugi only actually dueled about 5 or 6 times during the entire series, all other times it was Atem. In order for Atem to cross over to the afterlife, he must be defeated by Yugi in an honest duel. If Atem wins, it means Yugi is ready to act in Atem's stead, if not, Atem must remain behind because it means Yugi is not ready or good enough yet to fulfill the roles Atem has played. t's a very close duel, and Atem makes a movie that would allow him to finish Yugi off, but Yugi, knowing how Atem thinks, anticipates the move and counters it, allowing him defeat Atem. Finally free of his duties, Atem departs for the afterlife, where he is greeted by all his friends from 5000 years ago.